Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids [scATAC-seq]

Disruptions in the tightly regulated process of human brain development have been linked to increased risk for brain and mental illnesses. While the genetic contribution to these diseases is well established, important environmental factors have been less studied at molecular and cellular levels. In this study, we used single-cell and cell-type-specific techniques to investigate the effect of glucocorticoid (GC) exposure, a mediator of antenatal environmental risk, on gene regulation and lineage specification in unguided human neural organoids. We characterized the transcriptional response to chronic GC exposure during neural differentiation and studied the underlying gene regulatory networks by integrating single-cell transcriptomics- with chromatin accessibility data. We found lasting cell type-specific changes that included autism risk genes and several transcription factors associated with neurodevelopment. Chronic GCs influenced lineage specification primarily by priming the inhibitory neuron lineage through key transcription factors like PBX3. We provide evidence for convergence of genetic and environmental risk factors through a common mechanism of altering lineage specification. Overall design: Single-cell ATAC sequencing (10x Genomics) was performed in neural organoids derived from the 409b2 iPSC line. Organoids were either chronically treated (Dexamethasone 100nM, Chr-Veh condition) or vehicle-exposed (DMSO, Veh-Veh condition) for 10 days (day 60 - 70) and collected at day 90 following a 20-day washout period and an additional 12 hour acute exposure to the treatment vehicle DMSO. Four biological replicates were collected for each condition.